OpenRaiser/Intern-Atlas huggingface dataset:
scRDiT: Generating single-cell RNA-seq data by diffusion transformers and accelerating sampling
Venue: arXiv cs.LG 2024
Year: 2024

Motivation: Single-cell RNA sequencing (scRNA-seq) is a groundbreaking technology extensively utilized in biological research, facilitating the examination of gene expression at the individual cell level within a given tissue sample. While numerous tools have been developed for scRNA-seq data analysis, the challenge persists in capturing the distinct features of such data and replicating virtual datasets that share analogous statistical properties. Results: Our study introduces a generative approach termed scRNA-seq Diffusion Transformer (scRDiT). This method generates virtual scRNA-seq data by leveraging a real dataset. The method is a neural network constructed based on Denoising Diffusion Probabilistic Models (DDPMs) and Diffusion Transformers (DiTs). This involves subjecting Gaussian noises to the real dataset through iterative noise-adding steps and ultimately restoring the noises to form scRNA-seq samples. This scheme allows us to learn data features from actual scRNA-seq samples during model training. Our experiments, conducted on two distinct scRNA-seq datasets, demonstrate superior performance. Additionally, the model sampling process is expedited by incorporating Denoising Diffusion Implicit Models (DDIM). scRDiT presents a unified methodology empowering users to train neural network models with their unique scRNA-seq datasets, enabling the generation of numerous high-quality scRNA-seq samples. Availability and implementation: https://github.com/DongShengze/scRDiT
WaSP: Warp Scheduling to Mimic Prefetching in Graphics Workloads
Venue: arXiv cs.AR 2024
Year: 2024

Contemporary GPUs are designed to handle long-latency operations effectively; however, challenges such as core occupancy (number of warps in a core) and pipeline width can impede their latency management. This is particularly evident in Tile-Based Rendering (TBR) GPUs, where core occupancy remains low for extended durations. To address this challenge, we introduce WaSP, a lightweight warp scheduler tailored for GPUs in graphics applications. WaSP strategically mimics prefetching by initiating a select subset of warps, termed priority warps, early in execution to reduce memory latency for subsequent warps. This optimization taps into the inherent but underutilized memory parallelism within the GPU core. This underutilization is a consequence of a baseline scheduler that evenly spaces misses throughout execution to exploit the inherent spatial locality in graphics workloads. WaSP improves on this by reducing average memory latency while maintaining locality for the majority of warps. While maximizing memory parallelism utilization, WaSP prevents saturating the caches with misses to avoid filling up the MSHRs (Miss Status Holding Registers). This approach reduces cache stalls that halt further accesses to the cache. Overall, WaSP yields a significant 3.9% performance speedup. Importantly, WaSP accomplishes these enhancements with a negligible overhead, positioning it as a promising solution for enhancing the efficiency of GPUs in managing latency challenges.
YOLC: You Only Look Clusters for Tiny Object Detection in Aerial Images
Venue: arXiv cs.CV 2024
Year: 2024

Detecting objects from aerial images poses significant challenges due to the following factors: 1) Aerial images typically have very large sizes, generally with millions or even hundreds of millions of pixels, while computational resources are limited. 2) Small object size leads to insufficient information for effective detection. 3) Non-uniform object distribution leads to computational resource wastage. To address these issues, we propose YOLC (You Only Look Clusters), an efficient and effective framework that builds on an anchor-free object detector, CenterNet. To overcome the challenges posed by large-scale images and non-uniform object distribution, we introduce a Local Scale Module (LSM) that adaptively searches cluster regions for zooming in for accurate detection. Additionally, we modify the regression loss using Gaussian Wasserstein distance (GWD) to obtain high-quality bounding boxes. Deformable convolution and refinement methods are employed in the detection head to enhance the detection of small objects. We perform extensive experiments on two aerial image datasets, including Visdrone2019 and UAVDT, to demonstrate the effectiveness and superiority of our proposed approach. Code is available at https://github.com/dawn-ech/YOLC.
EPL: Evidential Prototype Learning for Semi-supervised Medical Image Segmentation
Venue: arXiv cs.CV 2024
Year: 2024

Although current semi-supervised medical segmentation methods can achieve decent performance, they are still affected by the uncertainty in unlabeled data and model predictions, and there is currently a lack of effective strategies that can explore the uncertain aspects of both simultaneously. To address the aforementioned issues, we propose Evidential Prototype Learning (EPL), which utilizes an extended probabilistic framework to effectively fuse voxel probability predictions from different sources and achieves prototype fusion utilization of labeled and unlabeled data under a generalized evidential framework, leveraging voxel-level dual uncertainty masking. The uncertainty not only enables the model to self-correct predictions but also improves the guided learning process with pseudo-labels and is able to feed back into the construction of hidden features. The method proposed in this paper has been experimented on LA, Pancreas-CT and TBAD datasets, achieving the state-of-the-art performance in three different labeled ratios, which strongly demonstrates the effectiveness of our strategy.
The impact of data set similarity and diversity on transfer learning success in time series forecasting
Venue: arXiv cs.LG 2024
Year: 2024

Pre-trained models have become pivotal in enhancing the efficiency and accuracy of time series forecasting on target data sets by leveraging transfer learning. While benchmarks validate the performance of model generalization on various target data sets, there is no structured research providing similarity and diversity measures to explain which characteristics of source and target data lead to transfer learning success. Our study pioneers in systematically evaluating the impact of source-target similarity and source diversity on zero-shot and fine-tuned forecasting outcomes in terms of accuracy, bias, and uncertainty estimation. We investigate these dynamics using pre-trained neural networks across five public source datasets, applied to forecasting five target data sets, including real-world wholesales data. We identify two feature-based similarity and diversity measures, finding that source-target similarity reduces forecasting bias, while source diversity improves forecasting accuracy and uncertainty estimation, but increases the bias.
Open-Source AI-based SE Tools: Opportunities and Challenges of Collaborative Software Learning
Venue: arXiv cs.SE 2024
Year: 2024

Large Language Models (LLMs) have become instrumental in advancing software engineering (SE) tasks, showcasing their efficacy in code understanding and beyond. Like traditional SE tools, open-source collaboration is key in realising the excellent products. However, with AI models, the essential need is in data. The collaboration of these AI-based SE models hinges on maximising the sources of high-quality data. However, data especially of high quality, often holds commercial or sensitive value, making it less accessible for open-source AI-based SE projects. This reality presents a significant barrier to the development and enhancement of AI-based SE tools within the software engineering community. Therefore, researchers need to find solutions for enabling open-source AI-based SE models to tap into resources by different organisations. Addressing this challenge, our position paper investigates one solution to facilitate access to diverse organizational resources for open-source AI models, ensuring privacy and commercial sensitivities are respected. We introduce a governance framework centered on federated learning (FL), designed to foster the joint development and maintenance of open-source AI code models while safeguarding data privacy and security. Additionally, we present guidelines for developers on AI-based SE tool collaboration, covering data requirements, model architecture, updating strategies, and version control. Given the significant influence of data characteristics on FL, our research examines the effect of code data heterogeneity on FL performance.
Privacy-preserving Scanpath Comparison for Pervasive Eye Tracking
Venue: arXiv cs.CR 2024
Year: 2024

As eye tracking becomes pervasive with screen-based devices and head-mounted displays, privacy concerns regarding eye-tracking data have escalated. While state-of-the-art approaches for privacy-preserving eye tracking mostly involve differential privacy and empirical data manipulations, previous research has not focused on methods for scanpaths. We introduce a novel privacy-preserving scanpath comparison protocol designed for the widely used Needleman-Wunsch algorithm, a generalized version of the edit distance algorithm. Particularly, by incorporating the Paillier homomorphic encryption scheme, our protocol ensures that no private information is revealed. Furthermore, we introduce a random processing strategy and a multi-layered masking method to obfuscate the values while preserving the original order of encrypted editing operation costs. This minimizes communication overhead, requiring a single communication round for each iteration of the Needleman-Wunsch process. We demonstrate the efficiency and applicability of our protocol on three publicly available datasets with comprehensive computational performance analyses and make our source code publicly accessible.
Quantum Circuit $C^*$-algebra Net
Venue: arXiv cs.LG 2024
Year: 2024

This paper introduces quantum circuit $C^*$-algebra net, which provides a connection between $C^*$-algebra nets proposed in classical machine learning and quantum circuits. Using $C^*$-algebra, a generalization of the space of complex numbers, we can represent quantum gates as weight parameters of a neural network. By introducing additional parameters, we can induce interaction among multiple circuits constructed by quantum gates. This interaction enables the circuits to share information among them, which contributes to improved generalization performance in machine learning tasks. As an application, we propose to use the quantum circuit $C^*$-algebra net to encode classical data into quantum states, which enables us to integrate classical data into quantum algorithms. Numerical results demonstrate that the interaction among circuits improves performance significantly in image classification, and encoded data by the quantum circuit $C^*$-algebra net are useful for downstream quantum machine learning tasks.
A Semantic Proof of Generalised Cut Elimination for Deep Inference
Venue: arXiv cs.LO 2024
Year: 2024

Multiplicative-Additive System Virtual (MAV) is a logic that extends Multiplicative-Additive Linear Logic with a self-dual non-commutative operator expressing the concept of "before" or "sequencing". MAV is also an extenson of the the logic Basic System Virtual (BV) with additives. Formulas in BV have an appealing reading as processes with parallel and sequential composition. MAV adds internal and external choice operators. BV and MAV are also closely related to Concurrent Kleene Algebras. Proof systems for MAV and BV are Deep Inference systems, which allow inference rules to be applied anywhere inside a structure. As with any proof system, a key question is whether proofs in MAV can be reduced to a normal form, removing detours and the introduction of structures not present in the original goal. In Sequent Calcluli systems, this property is referred to as Cut Elimination. Deep Inference systems have an analogous Cut rule and other rules that are not present in normalised proofs. Cut Elimination for Deep Inference systems has the same metatheoretic benefits as for Sequent Calculi systems, including consistency and decidability. Proofs of Cut Elimination for BV, MAV, and other Deep Inference systems present in the literature have relied on intrincate syntactic reasoning and complex termination measures. We present a concise semantic proof that all MAV proofs can be reduced to a normal form avoiding the Cut rule and other "non analytic" rules. We also develop soundness and completeness proofs of MAV (and BV) with respect to a class of models. We have mechanised all our proofs in the Agda proof assistant, which provides both assurance of their correctness as well as yielding an executable normalisation procedure.- Our technique extends to include exponentials and the additive units.
Design and Characterization of Strategy-Proof Mechanisms for Two-Facility Game on a Line
Venue: arXiv cs.GT 2024
Year: 2024

We focus on the problem of placing two facilities along a linear space to serve a group of agents. Each agent is committed to minimizing the distance between her location and the closest facility. A mechanism is an algorithm that maps the reported agent locations to the facility locations. We are interested in mechanisms without money that are deterministic, strategy-proof, and provide a bounded approximation ratio for social cost. It is a fundamental problem to characterize the family of strategy-proof mechanisms with a bounded approximation ratio. Fotakis and Tzamos already demonstrated that the deterministic strategy-proof mechanisms for the 2-facility game problem are mechanisms with a unique dictator and the leftmost-rightmost mechanism. In this paper, we first present a more refined characterization of the first family. We then reveal three new classes of strategy-proof mechanisms that show the intricacy of structure within this family. This helps us get a more complete picture of the characterization of the 2-facility game problem, and may also have value in understanding and solving more general facility allocation game problems. Besides, based on our refined characterization, we surprisingly find that prediction cannot effectively improve the performance of the mechanism in the two-facility game problem, while this methodology to overcome bad approximation ratio works in many other mechanism design problems. We show that if we require that the mechanism admits a bounded approximation ratio when the prediction is arbitrarily bad, then at the same time, the mechanism can never achieve sublinear approximation ratios even with perfect prediction.
DDPG-E2E: A Novel Policy Gradient Approach for End-to-End Communication Systems
Venue: arXiv cs.NI 2024
Year: 2024

The End-to-end (E2E) learning-based approach has great potential to reshape the existing communication systems by replacing the transceivers with deep neural networks. To this end, the E2E learning approach needs to assume the availability of prior channel information to mathematically formulate a differentiable channel layer for the backpropagation (BP) of the error gradients, thereby jointly optimizing the transmitter and the receiver. However, accurate and instantaneous channel state information is hardly obtained in practical wireless communication scenarios. Moreover, the existing E2E learning-based solutions exhibit limited performance in data transmissions with large block lengths. In this article, these practical issues are addressed by our proposed deep deterministic policy gradient-based E2E communication system. In particular, the proposed solution utilizes a reward feedback mechanism to train both the transmitter and the receiver, which alleviates the information loss of error gradients during BP. In addition, a convolutional neural network (CNN)-based architecture is developed to mitigate the curse of dimensionality problem when transmitting messages with large block lengths. Extensive simulations then demonstrate that our proposed solution can not only jointly train the transmitter and the receiver simultaneously without requiring the prior channel knowledge but also can obtain significant performance improvement on block error rate compared to state-of-the-art solutions.
Statistical Modelling of Driving Scenarios in Road Traffic using Fleet Data of Production Vehicles
Venue: arXiv cs.RO 2024
Year: 2024

Ensuring the safety of road vehicles at an acceptable level requires the absence of any unreasonable risk arising from all potential hazards linked to the intended au-tomated driving function and its implementation. The assurance that there are no unreasonable risks stemming from hazardous behaviours associated to functional insufficiencies is denoted as safety of intended functionality (SOTIF), a concept outlined in the ISO 21448 standard. In this context, the acquisition of real driving data is considered essential for the verification and validation. For this purpose, we are currently developing a method with which data collect-ed representatively from production vehicles can be modelled into a knowledge-based system in the future. A system that represents the probabilities of occur-rence of concrete driving scenarios over the statistical population of road traffic and makes them usable. The method includes the qualitative and quantitative ab-straction of the drives recorded by the sensors in the vehicles, the possibility of subsequent wireless transmission of the abstracted data from the vehicles and the derivation of the distributions and correlations of scenario parameters. This paper provides a summary of the research project and outlines its central idea. To this end, among other things, the needs for statistical information and da-ta from road traffic are elaborated from ISO 21448, the current state of research is addressed, and methodical aspects are discussed.
Audio-Visual Generalized Zero-Shot Learning using Pre-Trained Large Multi-Modal Models
Venue: arXiv cs.CV 2024
Year: 2024

Audio-visual zero-shot learning methods commonly build on features extracted from pre-trained models, e.g. video or audio classification models. However, existing benchmarks predate the popularization of large multi-modal models, such as CLIP and CLAP. In this work, we explore such large pre-trained models to obtain features, i.e. CLIP for visual features, and CLAP for audio features. Furthermore, the CLIP and CLAP text encoders provide class label embeddings which are combined to boost the performance of the system. We propose a simple yet effective model that only relies on feed-forward neural networks, exploiting the strong generalization capabilities of the new audio, visual and textual features. Our framework achieves state-of-the-art performance on VGGSound-GZSL, UCF-GZSL, and ActivityNet-GZSL with our new features. Code and data available at: https://github.com/dkurzend/ClipClap-GZSL.
Experimental System Design of an Active Fault-Tolerant Quadrotor
Venue: arXiv cs.RO 2024
Year: 2024

Quadrotors have gained popularity over the last decade, aiding humans in complex tasks such as search and rescue, mapping and exploration. Despite their mechanical simplicity and versatility compared to other types of aerial vehicles, they remain vulnerable to rotor failures. In this paper, we propose an algorithmic and mechanical approach to addressing the quadrotor fault-tolerant problem in case of rotor failures. First, we present a fault-tolerant detection and control scheme that includes various attitude error metrics. The scheme transitions to a fault-tolerant control mode by surrendering the yaw control. Subsequently, to ensure compatibility with platform sensing constraints, we investigate the relationship between variations in robot rotational drag, achieved through a modular mechanical design appendage, resulting in yaw rates within sensor limits. This analysis offers a platform-agnostic framework for designing more reliable and robust quadrotors in the event of rotor failures. Extensive experimental results validate the proposed approach providing insights into successfully designing a cost-effective quadrotor capable of fault-tolerant control. The overall design enhances safety in scenarios of faulty rotors, without the need for additional sensors or computational resources.
Towards Practical Meshlet Compression
Venue: arXiv cs.GR 2024
Year: 2024

We propose a codec specifically designed for meshlet compression, optimized for rapid data-parallel GPU decompression within a mesh shader. Our compression strategy orders triangles in optimal generalized triangle strips (GTSs), which we generate by formulating the creation as a mixed integer linear program (MILP). Our method achieves index buffer compression rates of 16:1 compared to the vertex pipeline and crack-free vertex attribute quantization based on user preference. The 15.5 million triangles of our teaser image decompress and render in 0.59 ms on an AMD Radeon RX 7900 XTX.
Test-Time Adaptation with SaLIP: A Cascade of SAM and CLIP for Zero shot Medical Image Segmentation
Venue: arXiv cs.CV 2024
Year: 2024

The Segment Anything Model (SAM) and CLIP are remarkable vision foundation models (VFMs). SAM, a prompt driven segmentation model, excels in segmentation tasks across diverse domains, while CLIP is renowned for its zero shot recognition capabilities. However, their unified potential has not yet been explored in medical image segmentation. To adapt SAM to medical imaging, existing methods primarily rely on tuning strategies that require extensive data or prior prompts tailored to the specific task, making it particularly challenging when only a limited number of data samples are available. This work presents an in depth exploration of integrating SAM and CLIP into a unified framework for medical image segmentation. Specifically, we propose a simple unified framework, SaLIP, for organ segmentation. Initially, SAM is used for part based segmentation within the image, followed by CLIP to retrieve the mask corresponding to the region of interest (ROI) from the pool of SAM generated masks. Finally, SAM is prompted by the retrieved ROI to segment a specific organ. Thus, SaLIP is training and fine tuning free and does not rely on domain expertise or labeled data for prompt engineering. Our method shows substantial enhancements in zero shot segmentation, showcasing notable improvements in DICE scores across diverse segmentation tasks like brain (63.46%), lung (50.11%), and fetal head (30.82%), when compared to un prompted SAM. Code and text prompts are available at: https://github.com/aleemsidra/SaLIP.
MuPT: A Generative Symbolic Music Pretrained Transformer
Venue: arXiv cs.SD 2024
Year: 2024

In this paper, we explore the application of Large Language Models (LLMs) to the pre-training of music. While the prevalent use of MIDI in music modeling is well-established, our findings suggest that LLMs are inherently more compatible with ABC Notation, which aligns more closely with their design and strengths, thereby enhancing the model's performance in musical composition. To address the challenges associated with misaligned measures from different tracks during generation, we propose the development of a Synchronized Multi-Track ABC Notation (SMT-ABC Notation), which aims to preserve coherence across multiple musical tracks. Our contributions include a series of models capable of handling up to 8192 tokens, covering 90% of the symbolic music data in our training set. Furthermore, we explore the implications of the Symbolic Music Scaling Law (SMS Law) on model performance. The results indicate a promising direction for future research in music generation, offering extensive resources for community-led research through our open-source contributions.